Wednesday, January 21, 2015

SNP Prophet

If you had done your autosomal DNA testing and you want to know the genotype of an untested SNP, this is the tool. SNP prophet predicts your genotype for an untested SNP using your autosomal DNA. It has an offline version and an online version.The offline is huge but does not require any internet, nor depends on 3rd party services to be available on the internet, since everything it requires will be present in your computer. The online version however is extremely less is size but entirely depends on 3rd party APIs (OpenSNP's JSON and DAS) and their service availability. The tool supports FTDNA, Ancestry and 23andMe files.

Usage: Select the autosomal DNA file, enter the SNP you want to know it's genotype and click 'Find GenoType'. The total process for both online and offline can take sometimes 5 to 10 minutes.

Prerequisites: Microsoft .Net Framework 4.0

Screenshot:

Download :


Source Code:


Change Log
    Version 1.0
    • Initial Release.

    Tyrolean Ancient DNA

    The Tyrolean Iceman, a 5300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Oetztal Alps. The authors sequenced the complete genome of the Iceman. The authors had mentioned in the paper that they were able to extract 125,729 SNPs from all samples. I was able to convert only 2 samples ERR107308 and ERR107309 due to technical limitations.

    Download: 
    Reference:
    Keller, Andreas, et al. "New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing." Nature communications 3 (2012): 698.

    Data Used

    Monday, January 19, 2015

    GEDmatch Plus for Google Chrome


    Note: The chrome extension accesses GEDMatch website (gedmatch.com) to get details but GEDMatch neither supports nor promotes its use in any way.


    GEDmatch Plus is a chrome browser extension that adds additional functionality for GEDmatch website (www.gedmatch.com) like themes and caching.

    The extension adds a number of features to GEDmatch:

    • Several Themes, Styles etc
    • Caching of 1-to-Many, 1-to-1 Autosomal and 1-to-1 X-DNA, to reduce server load and boost performance. Caches are automatically expired after 7 days.


    Prerequisites: Google Chrome

    Screenshots:


     

     

     


    Usage: Install the addon and go to Options page and select the theme you want. Caching is enabled by default.

    Install: GEDmatch Plus Chrome Extension

    Source Code at GitHub.

    Change Log :1.0.0
    • Initial Release.

    Saturday, January 10, 2015

    Segment Compatibility

    If you want to check the segment compatibility from different kit versions from DNA testing companies, (or) if you match someone on a particular segment on lower thresholds and you want to check if that result is due to different kit versions from DNA testing companies, then this is the tool. It supports FTDNA's Affymetrix and Illumina, 23andMe's V2, V3, V4 and Ancestry files.

    Usage: To use this tool, select your kit version, your match's kit version and enter the segment details like chromosome, start and end positions. The positions should be in build 37/hg19. Then click 'Verify' button. A message box will popup to say pass/fail for the segment which is based on the requirement of atleast 100 SNPs per Mb for the specified segment. The below grid will display the available SNPs in each kit version and further below that, you find the overlapping SNP count. You can also download detailed information on the specified segment.

    Prerequisites: Microsoft .Net Framework 4.0

    Screenshot:


    Download : Segment Compatibility.exe (10.2 MB)

    Source Code at GitHub.

    Change Log
      Version 1.0
      • Initial Release.

      Thursday, January 1, 2015

      Sub Project: Autosomal Tree Visualizer

      This is a sub-project for Autosomal Pedigree Creator.

      This tool allows to visualize triangulated segments on autosomal pedigree trees. This tool is very similar to Ancient Ancestry and has all features of it, except instead of triangulated segments from ancient kits, it contains triangulated segments from the kits you select.

      Prerequisites:
      Usage:

      1. Copy the downloaded executable into Autosomal Pedigree Creator root folder. 
      2. Execute the file and it will prompt you to select the kits folder. This folder is the same folder used to generate the pedigree using Autosomal Pedigree Creator.
      3. Please wait until the kits are loaded. You can see the progress in the status bar.
      4. Once loaded, you can open entirely a different kit (a potential match) and see how segments match the kits in the pedigree.

      Screenshot:

       

      Download Autosomal Tree Visualizer.exe (686 KB)

      Source Code at GitHub.

      License: MIT License.